398 research outputs found

    Texture analysis of corpora lutea in ultrasonographic ovarian images using genetic programming and rotation invariant local binary patterns

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    Ultrasonography is widely used in medical diagnosis with the advantages of being low cost, non-invasive and capable of real time imaging. When interpreting ultrasonographic images of mammalian ovaries, the structures of interest are follicles, corpora lutea (CL) and stroma. This thesis presents an approach to perform CL texture analysis, including detection and segmentation, based on the classifiers trained by genetic programming (GP). The objective of CL detection is to determine whether there is a CL in the ovarian images, while the goal of segmentation is to localize the CL within the image. Genetic programming (GP) offers a solution through the evolution of computer programs by methods inspired by the mechanisms of natural selection. Herein, we use rotationally invariant local binary patterns (LBP) to encode the local texture features. These are used by the programs which are manipulated by GP to obtain highly fit CL classifiers. Grayscale standardization was performed on all images in our data set based on the reference grayscale in each image. CL classification programs were evolved by genetic programming and tested on ultrasonographic images of ovaries. On the bovine dataset, our CL detection algorithm is reliable and robust. The detection algorithm correctly determined the presence or absence of a CL in 93:3% of 60 test images. The segmentation algorithm achieved a mean (± standard deviation) sensitivity and specificity of 0:87 ± 0:14 and 0:91 ± 0:05, respectively, over the 30 CL images. Our CL segmentation algorithm is an improvement over the only previously published algorithm, since our method is fully automatic and does not require the placement of an initial contour. The success of these algorithms demonstrates that similar algorithms designed for analysis of in vivo human ovaries are likely viable

    Classification of bovine reproductive cycle phases using ultrasound-detected features

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    With the combination of computer-assisted image analysis and ultrasonographic imaging technology, it has been possible to study and increase the knowledge in different areas of medicine. Studies of ovarian development in female mammals using ultrasonography have shown a relationship between the day in the estrous cycle and the main structures of the ovary.Ultrasound images of bovine ovaries were used to determine whether ultrasound-detected features can automatically determine the phase in the estrous cycle based on a single day's ultrasound examination of the ovaries. Five ultrasound-detected features of the bovine ovaries were used to determine the phase in the estrous cycle: (1) size of the dominant follicle; (2) size of the first subordinate follicle; (3) size of the second subordinate follicle; (4) size of the corpus luteum and (5) number of subordinate follicles with size ≥ 2mm. The collection of ultrasound images used for this study was formed by a group of 45 pairs of ovaries (left and right) which were imaged on day 3, day = 10 and day ≥ 17 of the estrous cycle corresponding to the metestrus, diestrus and proestrus phases respectively.Four different experiments were performed to test the hypothesis. For experiments 1, 2 and 3 the bovine ovaries were classified into three different classes: day 3 of wave 1 (D3W1), day 1 of wave 2 (D1W2) and day 17 or higher (D≥17) that were related to the follicular development of the ovary and the estrous cycle phases as: metestrus, diestrus and proestrus respectively. For experiment 4 the bovine ovaries were classified into four classes: D3W1, D6W1, D1W2 and D≥17. The additional class (D6W1: day 6 of wave 1) was incorporated to represent the early-diestrus phase in the estrous cycle.Two classifiers were implemented for all experiments and their performances compared: a decision tree classifier and a naive Bayes classifier. The decision tree classifier had the best performance with a classification rate of 100% for experiments 1, 2 and 3, giving a rather simple decision tree which used only two features to make a classification: size of the dominant follicle and size of the corpus luteum, suggesting these are key features in distinguishing between phases in the estrous cycle giving the most relevant information. The naive Bayes had a classification rate of 86.36% for experiment 1, 95.55% for experiment 2 and 90% for experiment 3. The results of this study supported the hypothesis that by using ultrasound detected features of bovine ovaries we can determine automatically the stage in the estrous cycle based on a single day's examination

    3d acceleration for heat detection in dairy cows

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    Accurate and reliable detection of heat in dairy cows is essential for a controlled reproduction and therefore, for maintaining milk production. Classical approaches like visual identification are no longer viable on large dairy herds. Several automated techniques of detection have been proposed, but expected results are only achieved by expensive or invasive methods, because practical methods are not reliable. We present a method that aims to be both practical and accurate. It is based on simple attributes extracted from 3D acceleration data and well known classifiers: multilayer perceptrons, support vector machines and decision trees. Results show promising detection ratios, above 90% in several configurations of the detection system. Best results are achieved with multilayer perceptrons. This information could be readily incorporated to the automated system in a dairy farm and help to improve its efficiency.Sociedad Argentina de Informática e Investigación Operativa (SADIO

    SaLSa : a combinatory approach of semi-automatic labeling and long short-term memory to classify behavioral syllables

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    Accurately and quantitatively describing mouse behavior is an important area. Although advances in machine learning have made it possible to track their behaviors accurately, reliable classification of behavioral sequences or syllables remains a challenge. In this study, we present a novel machine learning approach, called SaLSa (a combination of semi-automatic labeling and long short-term memory-based classification), to classify behavioral syllables of mice exploring an open field. This approach consists of two major steps: first, after tracking multiple body parts, spatial and temporal features of their egocentric coordinates are extracted. A fully automated unsupervised process identifies candidates for behavioral syllables, followed by manual labeling of behavioral syllables using a graphical user interface. Second, a long short-term memory (LSTM) classifier is trained with the labeled data. We found that the classification performance was marked over 97%. It provides a performance equivalent to a state-of-the-art model while classifying some of the syllables. We applied this approach to examine how hyperactivity in a mouse model of Alzheimer's disease (AD) develops with age. When the proportion of each behavioral syllable was compared between genotypes and sexes, we found that the characteristic hyper-locomotion of female AD mice emerges between 4 and 8 months. In contrast, age-related reduction in rearing is common regardless of genotype and sex. Overall, SaLSa enables detailed characterization of mouse behavior

    Evaluation of texture features for analysis of ovarian follicular development

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    Ovarian follicles in women are fluid-filled structures in the ovary that contain oocytes (eggs). A dominant follicle is physiologically selected and ovulates during the menstrual cycle. We examined the echotexture in ultrasonographic images of the follicle wall of dominant ovulatory follicles in women during natural menstrual cycles and dominant anovulatory follicles which developed in women using oral contraceptives (OC). Texture features of follicle wall regions of both ovulatory and anovulatory dominant follicles were evaluated over a period of seven days before ovulation (natural cycles) or peak estradiol concentrations (OC cycles). Differences in echotexture between the two classes of follicles were found for two co-occurrence matrix derived texture features and two edge-frequency based texture features. Co-occurrence energy and homogeneity were significantly lower for ovulatory follicles while edge density and edge contrast were higher for ovulatory follicles. In the each feature space, the two classes of follicle were adequately separable.This thesis employed several statistical approaches to analyses of texture features, such as plotting method and the Mann-Kendall method. A distinct change of feature trend was detected 3 or 4 days before the day of ovulation for ovulatory follicles in the two co-occurrence matrix derived texture features and two edge-frequency-based texture features. Anovulatory follicles, exhibited the biggest variation of the feature value 3 or 4 days before the day on which dominant follicles developed to maximum size. This discovery is believed to correspond to the ovarian follicles responding to system hormonal changes leading to presumptive ovulation

    Mare endometrium : physiological and pathological involvement of hormones and neutrophil extracellular traps

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    Tese de Doutoramento em Ciências Veterinárias, Especialidade de Ciências Biológicas e Biomédicas.Two reproductive topics in mares were addressed in this thesis. The aims of the studies were to evaluate: (i) the effect of chronic oxytocin administration to mid-luteal phase mares on luteal maintenance and its cellular and molecular mechanisms at endometrial level; (ii) the capacity of equine neutrophils to produce neutrophil extracellular traps (NETs) in vitro when stimulated with bacteria obtained from mares with endometritis, and to determine if NETs release also occurred in vivo in mares with endometritis; (iii) the in vitro effects of some NETs components on mare endometrial fibrogenic capacity and to determine if they could depend on endometrial inflammatory lesions or estrous cycle phases; and (iv) the involvement of PGF2α and PGE2 pathways in collagen deposition on mare endometrium, challenged with NETs proteases. In the first study, luteal maintenance occurred in 67% of oxytocin treated mares, which may be related to oxytocin and progesterone (PGR) receptors spatial expression in endometrium. Reduction of endometrial estrogen receptor 2 (ESR2) may be responsible for the maintenance of PGR in luminal and glandular epithelium and may attenuate ESR1 endometrial transcriptional activity. Equine neutrophils were able to release NETs in the presence of bacteria that cause mare endometritis, and might be a complementary mechanism to fight endometritis. By in vitro studies with NETs proteases, increased collagen type I (COL1) production characteristic of fibrosis was observed, although endometrial response to each NETs protease depended on estrous cycle and/or endometrial category. Also, NETs proteases were linked to fibrogenesis, by increased synthesis of PGF2a and/or PGF2a receptor transcripts and impaired PGE2 or PGE2 receptor 2 transcripts associated to increased COL1. These effects were influenced by endometrium type and estrous cycle phases. Injury induced-changes on PG mediators by NETs components may instigate PGF2α or PGE2 vias, as additional pathways in mare endometrial fibrogenesis.RESUMO - Endométrio da égua: envolvimento fisiológico e patológico de hormonas e de redes extracelulares de neutrófilos - Nesta tese foram abordados dois temas reprodutivos em éguas. Os objectivos destes estudos consistiram na avaliação: (i) da administração crónica de ocitocina na manutenção do corpo lúteo em éguas na fase lútea média, e os mecanismos celulares e moleculares no endométrio; (ii) da capacidade dos neutrófilos equinos para produzirem redes extracelulares de neutrófilos (NETs) in vitro e in vivo quando estimulados com bactérias de éguas com endometrite; (iii) dos efeitos in vitro de componentes das NETs na fibrogénese do endométrio equino e sua associação com lesões inflamatórias no endométrio ou com o ciclo éstrico; e (iv) do envolvimento das vias da PGF2α e PGE2 na deposição de colagénio no endométrio da égua, incubado com proteases das NETs. No primeiro estudo, o prolongamento da função lútea em 67% das éguas tratadas com ocitocina, parece estar relacionado com alteração da expressão espacial dos receptores de ocitocina e progesterona (PGR) no endométrio. A diminuição do receptor 2 dos estrogénios (ESR2) pode ser responsável pela manutenção do PGR no epitélio luminal e glandular do endométrio e atenuar a transcrição do ESR1. Os neutrófilos equinos libertaram NETs na presença de bactérias causadoras de endometrite podendo ser um mecanismo complementar no combate à endometrite. As proteases das NETs in vitro aumentaram a produção de colagénio do tipo I (COL1), característico de fibrose, no endométrio, embora a resposta a cada protease dependesse do ciclo éstrico e/ou da categoria do endométrio. O aumento do COL1 associado ao incremento de PGF2α e/ou da transcrição do seu receptor e à diminuição da PGE2 e/ou do seu receptor 2, parecem implicar as prostaglandinas e as proteases das NETs na fibrogénese no endométrio equino. Alterações nos mediadores das prostaglandinas, induzidas pelos componentes das NETs, podem instigar as vias da PGF2a ou da PGE2, como mecanismos adicionais de fibrose do endométrio da égua.N/

    Simultaneous alterations in ovaries and bone as a result of Polycystic Ovary Syndrome

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    Polycystic ovary syndrome (PCOS) is one of the most widely recognized endocrine disorders affecting reproductive-age women. The etiopathogenesis and mechanisms of this syndrome remain unclear. Diagnosis requires two of the following: polycystic ovaries, oligo- or anovulation, and hyperandrogenism. Most women with PCOS display conditions such as metabolic abnormalities, diabetes, obesity, cardiovascular disease, and/or bone dysfunction. Considering the ethical limitations of human studies, animal and cell culture models that reflect some features of PCOS are important for investigation of this syndrome. The aim of the present work was to study some of the endocrine relationships between ovaries and bone tissue in a polycystic ovary syndrome animal model. The study was performed using an estradiol valerate PCOS-induced rat model (n = 30) and bone mesenchymal stem cell cultured from bone marrow of those animals. It was hypothesized that changes of the endocrine relationship between ovaries and bones could be observed in from in vivo animal model and in vitro cell culture assays. The ovarian morphological and endocrine changes seem to be correlated with endocrine, biophysical, and biomechanical changes in bone properties. Mesenchymal stem cells obtained from PCOS-induced rats, cultured for up to 21 days and differentiated into osteoblasts, presented lower viability and reduced mineralization of the extracellular matrix. Taken together, these results indicate important endocrine and structural effects of PCOS in ovaries and bones, contributing to part of the understanding of the pathophysiological mechanisms of PCOS

    Temporal expression of protein mediators during PGF2alpha-induced luteolysis in sheep

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    To study dynamic in vivo biochemical changes within the corpus luteum (CL) during luteolysis, a physiological model mimicking the onset of natural luteolysis was established, in which sheep received sequential systemic pulses of PGF2alpha (20ug/min/lhr) at mid-luteal phase of the estrous cycle. We previously demonstrated that after one pulse of PGF2alpha, the protein levels of extracellular matrix (ECM) regulators, tissue inhibitors of metalloproteinases (TIMPs) -1 and -2 decreased dramatically within one hour of PGF2alpha infusion, while matrix metalloproteinase (MMP)-2 activity increased 4 hrs post infusion. In summary, the early and dramatic decrease in TIMP-1 and TIMP-2 proteins, accompanied by an increase in MMP-2 activity, indicate an extension and amplification by the second pulse of PGF2alpha on regulators of the ECM within the CL. These findings confirm a critical role for regulators of the ECM in mediating both structural and steroidogenic changes during physiological PGF2alpha-induced luteolysis in sheep. (Abstract shortened by UMI.)

    2017 Annual Research Symposium Abstract Book

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    2017 annual volume of abstracts for science research projects conducted by students at Trinity College
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